Simple repetitive DNA sequences are a widespread and abundant feature of genomic DNA. The following several features characterize such sequences: (1) they typically consist of a variety of repeated motifs of 1-10 bases--but may include much larger repeats as well; (2) larger repeat units often include shorter ones within them; (3) long polypyrimidine and poly-CA tracts are often found; and (4) tandem arrangements of closely related motifs are often found. We propose that slipped-strand mispairing events, in concert with unequal crossing-over, can readily account for all of these features. The frequent occurrence of long tandem repeats of particular motifs (polypyrimidine and poly-CA tracts) appears to result from nonrandom patterns of nucleotide substitution. We argue that the intrahelical process of slipped-strand mispairing is much more likely to be the major factor in the initial expansion of short repeated motifs and that, after initial expansion, simple tandem repeats may be predisposed to further expansion by unequal crossing-over or other interhelical events because of their propensity to mispair. Evidence is presented that single-base repeats (the shortest possible motifs) are represented by longer runs in mammalian introns than would be expected on a random basis, supporting the idea that SSM may be a ubiquitous force in the evolution of the eukaryotic genome. Simple repetitive sequences may therefore represent a natural ground state of DNA unselected for coding functions.

Slipped-strand mispairing: a major mechanism for DNA sequence evolution.

https://www.cell.com/cell/pdf/0092-8674(84)90440-9.pdf

Construction and applications of a highly transmissible murine retrovirus shuttle vector.

https://www.cell.com/cell/pdf/0092-8674(92)90477-T.pdf

Regulation of alternative pre-mRNA splicing by hnRNP A1 and splicing factor SF2

Pre-early adenovirus 5 gene product regulates synthesis of early viral messenger RNAs

In light of present progress in the understanding of how messenger RNA is constructed in eukaryotic cells, the levels of gene control are discussed. Transcriptional control, assessed by the rate of synthesis of specific nuclear RNA, is strongly indicated to be the most frequent level of control. Definition of eukaryotic transcription units as simple (encoding one protein} and complex (encoding two or more proteins) affords a framework in which to discuss control at the level of RNA processing for which several examples also are known. Finally, differential stability of cytoplasmic mRNAs and differential translation, both well established, are briefly described.

Variety in the level of gene control in eukaryotic cells

Regulation of the appearance of cytoplasmic RNAs from region 1 of the adenovirus 2 genome.

A method is described for the preparation isolation of highly purified adenovirus RNA species. Cytoplasmic RNAs from cells infected with adenovirus 2 were selected by hybridization to viral DNA fragments bound to nitrocellulose membranes. A series of washes at elevated temperatures (50-70 degrees) determined conditions at which the true hybrids were stable but non-specific RNA was removed. This temperature has been found to correlate with the base composition of the DNA fragment. After washing at this predetermined temperature, the specific RNA was eluted at 85 degrees. The purity of the eluted RNA was greater than 95% as determined by size, sequence specificity, and template activity in an in vitro protein synthesizing system. The method described should be generally useful for purification of specific RNAs.

Purification of specific adenovirus 2 RNAs by preparative hybridization and selective thermal elution

Late cytoplasmic RNAs specified by two regions of the adenovirus 2 genome (39.3--51.8 and 70.7--83.4 map units) were analyzed by size fractionation of poly(A)-[3H]RNA and subsequent hybridization to DNA fragments. Both regions encode RNAs whose sequence content exceeds the coding capacity of the region. These multiple transcripts are likely to function as mRNAs, because they are present on polyribosomes. The DNA segment 39.3--51.8 specifies 27S, 22S, and 18S RNAs. The genome sites specifying these three size classes were determined by hybridizations with seven different DNA fragments from this region of the genome. The 3' termini of all three size classes are specified by sequences near a common site, position 50.1. The 27S RNA includes sequences beginning near 39.3, the 22S RNA contains sequences from 41.0, and the 18S RNA includes sequences from approximately 45.3 on the unit genome. A second family of four RNAs is transcribed from 70.7--83.4. These 28S, 22S, 18S, and 16S RNAs have a relationship similar to the RNAs transcribed from 39.3--51.8. Sequences near the 5' ends of these four size classes are specified by different genome sites. However, the 3' termini of all four size classes were localized near map position 80.4. The synthesis of families of RNA may allow the translation of multiple polypeptides from a genome segment that has only one terminator site for mRNA synthesis.

Two regions of the adenovirus 2 genome specify families of late polysomal RNAs containing common sequences.

Adenovirus type 2 cytoplasmic RNAs synthesized late in productive infection were resolved by electrophoresis on formamide gels. Regions of the adenovirus 2 genome specifying RNAs of distinct size were determined by hybridization to specific DNA fragments generated by cleavage with endo R·EcoRI and endo R·SmaI. From these studies 13 distinct viral RNA species were identified. A 26S to 28S size class and a 21S to 23S size class were each found to consist of four distinct RNA species. Three RNA species were identified in a 16S to 18S size class, and a fourth size class, 11S to 13S, was resolved into two components. The SmaI-D region (0.38 to 0.51 on the unit genome) and the EcoRI-F, D region (0.70 to 0.83) of the genome were found to code for multiple transcripts. Three RNAs (28S, 22S, and 18S) are specified by SmaI-D, and four components, 28S, 22S, 18S, and 16S, are encoded by EcoRI-F,D. The RNA represented by each set of multiple transcripts exceeds the coding capacity of the respective region, and the species within each set of RNAs appear to contain common sequences. The relationship between the cytoplasmic RNA species synthesized at late times and early cytoplasmic RNAs was determined by hybridization-inhibition experiments. The multiple transcripts encoded by the EcoRI-D fragment were found to contain sequences that are present in early cytoplasmic RNA. These studies enabled preparation of a map which accounts for transcription of approximately 67% of the r strand of the adenovirus 2 genome.

Michael McGrogan

Papers

Regulation of the appearance of cytoplasmic RNAs from region 1 of the adenovirus 2 genome.

Purification of specific adenovirus 2 RNAs by preparative hybridization and selective thermal elution

Two regions of the adenovirus 2 genome specify families of late polysomal RNAs containing common sequences.

Species Identification and Genome Mapping of Cytoplasmic Adenovirus Type 2 RNAs Synthesized Late in Infection